If you go long in KiCAD, you need the following folders, preferably on a data share/drive and not on your os/system drive for more easy backup:
- symbols (currently .lib files, will become .sweet folders afaik with symbol files .kicad_sym? in them)
- footprints (.pretty folders which contain .kicad_mod files, which are the footprints)
- 3d models (suggest similar subfolders as for footprints, models are in .wlr files (VRML), but can be .igs (IGES) or .stp (STEP) in far future (*))
- projects (folder that contains subfolders - 1 per project, which contain .pro files and all the other files for a project (.sch. lib, .net, etc.pp)
- python scripts (for the scripts you use/download for KiCAD, this folder needs special hooking to get working with KiCAD)
That’s the baseline.
On top of this you might want/need/consider:
- datasheet folder (for footprints at least)
- how to folder (download guides/tutorials from the web here for kicad)
I don’t use pcb templates, don’t intend to, so I ignore them.
I once downloaded/got the public footprints, but removed them as I make my own as I go along.
Symbols I got the public ones loaded (still) but never used them, also made my own.
If I weren’t so proficient in 3d, I would probably use the public models, but yeah, I also use my own 
If you create gerbers/drill files, create a sub-directory in the project folder and output them into that one, makes it easier to zip them up for fabrication. I use just ‘/gerber’.
PS: If you look for stuff to download now and digest later:
- Rheingold Heavy has some articles on BOM and getting KiCAD projects fabrication ready
- Chris Gammell (Contextual Electronis) youtube channel (I used firefox and DownThemAll extension and stored them locally)
- get KiCost from github, made by @devbisme
- as you’re on windows, check out the nightly builds if you need/want the bleeding edge, but be prepared for bugs
- if you need collaboration with mechanical engineers check out StepUP from @maui and get used to have VRML + STEP files at hand for your projects